I am also indebted to the ChEMBL team (@chembl) for both providing such valuable data under a liberal Open Access license and their critical reading of the manuscript! Additionally, I would like to stress that the ChEMBL team will create their own RDF version of ChEMBL and that this paper is not describing the version they will release.

This paper outlines the RDF as it has evolved from various earlier projects. The above diagram visualizes the basic structure (red), various Linked Data resources linked too (blue) and illustrates how various ontologies are used, such as the CHEMINF, BIBO, and CiTO ontologies.

Additionally, various applications and links are described developed by various co-authors. For example, Peter worked on the use in Bio2RDF and Bin and David on Chem2Bio2RDF. Andra developed an extension for his (#altmetric) CitedIn resource, giving credit to a paper when data in it is extracted into ChEMBL. Ola, Valery, and Anthony developed a Bioclipse Decision Support extension, which supports a nearest neighbor search in ChEMBL using ChemSpider. Of course, Ola also hosts the SPARQL end point of which you can monitor the uptime at the also cool mondeca.com service:

(Yes, I think I have all the cool buzzwords covered in this paper. Sadly, marketing is needed nowadays as a scientist. Where is the time that you could rant on page after page in all your domain specific jargon, not having to worry if your reader would understand it immediately, or without a university degree...)

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This blog deals with chemblaics in the broader sense. Chemblaics (pronounced chem-bla-ics) is the science that uses computers to solve problems in chemistry, biochemistry and related fields. The big difference between chemblaics and areas such as chem(o)?informatics, chemometrics, computational chemistry, etc, is that chemblaics only uses open source software, open data, and open standards, making experimental results reproducible and validatable. And this is a big difference!

About Me

Assistant professor at Maastricht University, studying biology at an unsupervised but atomic level. Open science is my main hobby resulting in participation in, among many others, Bioclipse, CDK and Wikipathways.

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